Variant report

Variant	rs10779636
Chromosome Location	chr1:215232162-215232163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10746453	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10864147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864149	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10864151	0.81[CEU][hapmap]
rs11120480	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11120481	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11120482	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11120504	0.81[CEU][hapmap]
rs1157492	0.86[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11802959	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12028008	0.89[CEU][hapmap];0.91[CHB][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1349674	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1377183	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1452636	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1452638	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1901623	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2363563	0.84[CEU][hapmap]
rs4655271	0.81[CEU][hapmap]
rs6540882	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468105	chr1:215167236-215248417	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv549182	chr1:215167236-215248417	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10779636	KCNH1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215222800-215242200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:215228000-215233400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:215228000-215237200	Weak transcription	Pancreas	Pancrea
4	chr1:215229000-215233800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:215229200-215237800	Weak transcription	NHEK	skin
6	chr1:215229400-215253000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:215230600-215232200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:215231600-215247600	Weak transcription	NHDF-Ad	bronchial

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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